The current GATK version is 3.6-0
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Posts: 2Member

Is it possible to adjust the compression level of the BAM-files (like i picard etc). To optimize speed/disk long term disk usage, this would be advantageous when producing temporary/final BAM files, e.g. using the indelrealigner and printreads tools, respectively.

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I'm not aware of any functions within GATK to do that, sorry.

Geraldine Van der Auwera, PhD

Correction: my colleague points out that you can actually do that with the --bam_compression engine argument.

Geraldine Van der Auwera, PhD

• Posts: 96Member ✭✭✭

Is this information still correct? I've been looking around for --bam_compression in the engine arguments, but I can't find it.

Hmm, I'm not finding it in any of the engine argument collections either. I see it as a standalone in walkers like SplitSamFile, but my understanding was that it was available to any bam writer. Let me check with the team.

Geraldine Van der Auwera, PhD